BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084779.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,699,622 number of mapped reads = 1,543,337 (90.8%) number of supplementary alignments = 14,675 (0.86%) number of secondary alignments = 0 number of mapped bases = 103,738,086 bp number of sequenced bases = 103,697,707 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,133 duplication rate = 3.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8984 >>>>>>> ACTG content number of A's = 28,726,999 bp (27.7%) number of C's = 19,237,121 bp (18.55%) number of T's = 32,655,957 bp (31.49%) number of G's = 23,037,424 bp (22.22%) number of N's = 40,206 bp (0.04%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 893,645 number of insertions = 8,103 mapped reads with insertion percentage = 0.52% number of deletions = 24,637 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.63% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.2878X There is a 2.89% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9015468 0.03617029303208837 0.43968917584588985 chr2 243199373 8972626 0.03689411649922305 0.3478531353696047 chr3 198022430 6787758 0.03427772298319943 0.20762130084845073 chr4 191154276 7555167 0.03952392359771225 0.2333719744120178 chr5 180915260 6676375 0.036903327005140416 0.217081324800887 chr6 171115067 5822106 0.034024508198334164 0.23968323405691516 chr7 159138663 4706927 0.029577520077569083 0.27571589387450135 chr8 146364022 4670495 0.03191013020945817 0.340449114570632 chr9 141213431 4097263 0.029014683454578763 0.274195936439888 chr10 135534747 5015138 0.037002599783507915 0.2757125949055198 chr11 135006516 4442495 0.032905782117953475 0.2662769375099118 chr12 133851895 5067736 0.03786077141455487 0.22157279645586017 chr13 115169878 3290240 0.028568581100693706 0.19205242399062503 chr14 107349540 3170018 0.029529870365536733 0.20978367968285336 chr15 102531392 3344840 0.032622594258741755 0.20760731715991956 chr16 90354753 2456112 0.02718298615679908 0.21191209777789924 chr17 81195210 2728864 0.033608682088512365 0.2208274195647699 chr18 78077248 2996320 0.03837635260914934 0.6363582542969002 chr19 59128983 2176851 0.03681529580848702 0.32700898105175086 chr20 63025520 2181713 0.03461634271323743 0.2185999871255701 chr21 48129895 1407585 0.029245544790820758 0.20205908060509703 chr22 51304566 1383066 0.026957951461864037 0.18242138445176048 chrMT 16571 6139 0.37046647758131673 0.6591023631102593 chrX 155270560 5506906 0.035466517284409874 0.23430697546260618 chrY 59373566 259878 0.004376998342999981 0.10475381545127319